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NMMB tutorial Running NMMB Ratko Vasic NCWCP, April 1

st

2015

Retrieving model source code (SVN)

• https://svnemc.ncep.noaa.gov/projects/nems/trunk • Usage: #>svn co https://svnemc.ncep.noaa.gov/projects/nems/trunk • Directory structure: trunk: exe/ job_notused/ README README.GFS

README.NMM

README.TESTS

src/

tests/

Directory structure contd.

src:

atmos/

chem/

conf/ configure*

ENS_Cpl/ ESMFVersionDefine_ESMF_3.h

ESMFVersionDefine_ESMF_630rAPI.h

ESMFVersionDefine_ESMF_NUOPC.h

ESMFVersionLogic.h

MAIN_NEMS.F90

makefile module_EARTH_GENERIC_COMP.F90

module_EARTH_GRID_COMP.F90

module_EARTH_INTERNAL_STATE.F90

module_MEDIATOR.F90

module_NEMS_GRID_COMP.F90

module_NEMS_INTERNAL_STATE.F90

atmos: fim/ gen/ gsm/ io/ makefile module_ATM_GRID_COMP.F90

module_ATM_INTERNAL_STATE.F90

nmm/ phys/

post/ share/

Compilation on known machines: #> cd ~/trunk/src #> ./configure Run ./configure with one argument: 'configure 3_wcoss' : ESMF 3.1.0rp2 library on wcoss 'configure 3_zeus' : ESMF 3.1.0r series library (i.e. ESMF 3.1.0rp2, 3.1.0rp5) on zeus 'configure 3_gaea' : ESMF 3.1.0rp2 library on gaea 'configure 3_yellowstone' : ESMF 3.1.0rp2 library on yellowstone ....................

....................

#> ./configure 6_nmm_zeus #> make nmm #> ls –g ../exe total 30548 -rwxr-xr-x 1 ptmp 11801 Mar 28 00:05 mkDepends.pl

-rwxr-xr-x 1 ptmp 31248845 Mar 29 07:02

NEMS.x

•

Configure model

Configure directory #> cd ~/trunk/src/conf #> ls configure.nems.Gaea.intel

configure.nems.Gaea.pgi

configure.nems.Jet.ifort

configure.nems.Linux.g95

.......

modules.nems.Gaea_ESMF_NUOPC* modules.nems.wcoss_ESMF_3* modules.nems.wcoss_ESMF_630rAPI_gsm* modules.nems.wcoss_ESMF_630rAPI_nmm* .......

#> cat modules.nems.Zeus_ESMF_630rAPI_nmm

# This script is responsible for loading modules that are # compatible with the ESMF 6.3.0r API.

module purge module load mpt intel esmf/6.3.0rp1 netcdf

Configure model (contd.)

• Configure file (Snippet form configure.nems.Zeus.intel_12) SHELL = /bin/sh include $(ESMFMKFILE) ESMF_INC = $(ESMF_F90COMPILEPATHS) ESMF_LIB = $(ESMF_F90LINKPATHS) $(ESMF_F90LINKRPATHS) $(ESMF_F90ESMFLINKLIBS) NETCDF_INC = -I$(NETCDF)/include NETCDF_LIB = -L$(NETCDF)/lib -lnetcdf LIBDIR=/contrib/nceplibs/nwprod/lib NEMSIO_INC = -I${LIBDIR}/incmod/nemsio BACIO_LIB = -L${LIBDIR} -lbacio_4 EXTLIBS = $(NEMSIO_LIB) \ $(BACIO_LIB) \ FC = ifort -lmpi -openmp -convert big_endian -assume byterecl -mkl=sequential FPP = -fpp F77 = ifort -lmpi -openmp -convert big_endian -assume byterecl -mkl=sequential FREE = -free FIXED = -fixed R8 = -r8 FINCS = $(ESMF_INC) $(NEMSIO_INC) $(NETCDF_INC) TRAPS = #TRAPS = -g -fno-inline -no-ip -traceback -ftrapuv -fpe0 -ftz -check all -check noarg_temp_created -fp-stack-check FFLAGS = $(TRAPS) $(FINCS) -fp-model strict OPTS_NMM = -O3

Procedure summary:

• checkout model: svn co https://svnemc.ncep.noaa.gov/projects/nems/trunk • configure: cd ~/trunk/src ; ./configure 6_nmm_zeus • make: make nmm • executable: cd ~trunk/exe ; ls NEMS.x

Regression tests

• • More groups work on the same project Possibility of breaking other’s code #> cd ~trunk/tests #> ./rt.sh

Usage: ./rt.sh -c | -f | -s | -l | -m | -h -c create new baseline results for -f run full suite of regression tests -s run standard suite of regression tests -l runs test specified in -m compare against new baseline results -h display this help

Use of regression tests to run the model

#> cd ~trunk/tests #> more rt.conf

COMPILE | nmm_post | standard | wcoss | 6.3r_nmm | COMPILE | nmm | standard | zeus | 6_nmm | RUN | nmm_cntrl | standard | | nmm | RUN | nmm_nemsio | | | | RUN | nmm_rest | | | |

Use of regression tests to run the model

#> cd ~trunk/tests #> more rt.conf

COMPILE | nmm_post | standard | wcoss | 6.3r_nmm | COMPILE | nmm | standard | zeus | 6_nmm | RUN | nmm_cntrl | standard | | nmm | RUN | nmm_nemsio | | | | RUN | nmm_rest | | | |

Use of regression tests to run the model

#> cd ~trunk/tests #> more rt.conf

COMPILE | nmm | standard | zeus RUN | nmm_cntrl | 6_nmm | | standard | | nmm | #> ./rt.sh –s Three files: nmm_run nmm_qsub configure_file_01

Running model (nmm_run)

RUNDIR=_RUND_ SRCDIR=_SRCD_ mkdir -p $RUNDIR cd $RUNDIR cp _RTPWD_/NMMB_reg/input_nmmb_regional.d01_nemsio input_domain_01_nemsio cp _RTPWD_/NMMB_reg/nmmb_rst_01_nio_0024h_00m_00.00s restart_file_01_nemsio cp _RTPWD_/NMMB_reg/boco.* .

cp _RTPWD_/data/* .

cp $SRCDIR/tests/solver_state.txt .

elif [ $SCHEDULER = 'pbs' ]; then cp $SRCDIR/tests/nmm_qsub .

qsub nmm_qsub

Running model (nmm_qsub)

#!/bin/sh #PBS -o out #PBS -e err #PBS -N rt_31806_1 #PBS -A nems #PBS -l procs=48 #PBS -l walltime=00:15:00 export MPI_GROUP_MAX=96 export ESMF_RUNTIME_COMPLIANCECHECK=ON:depth=4 source .../modules.nems

module list cd $PBS_O_WORKDIR echo "Model started: " `date` mpiexec_mpt -prefix " %g:" -np $PBS_NP ./NEMS.x

echo "Model ended: " `date`

Running model (configure_file)

##### Grid Decomposition ##### inpes: 05 # Number of compute tasks in the I direction jnpes: 09 # Number of compute tasks in the J direction ##### Fundamental Timestep (seconds) ##### dt_int: 180 # Integer seconds dt_num: 0 # Numerator of fractional second dt_den: 1 # Denominator of fractional second nhours_fcst: 48 # Length of the forecast (hours) minutes_history: 180 # Frequency of history output (minutes) restart: false # True--> A restarted run minutes_restart: 720 # Frequency of restart output (minutes)

Running model (configure_file)

(contd.) global: true # True--> Global ; False--> Regional hydro: false # True--> Hydrostatic ; False--> Nonhydrostatic adiabatic: false # True--> Adiabatic ; False--> Diabatic shortwave: rrtm longwave: rrtm convection: bmj microphysics: fer_hires turbulence: myj sfc_layer: myj land_surface: noah # Radiation schemes # Convection scheme # Microphysics scheme # Turbulence schemes # Surface layer schemes # Land surface schemes nemsio_input: false write_hst_bin: true # True--> Write history files in binary format write_hst_nemsio: true # True--> Write history files in NEMSIO format write_rst_bin: true # True--> Write restart files in binary format write_rst_nemsio: true # True--> Write restart files in NEMSIO format

Adding new variable

• Adding local variable to internal state: Add it to a file: ~trunk/src/atmos/nmm/module_SOLVER_INTERNAL_STATE.F90

follow existing example i.e. “MAVAIL” REAL(kind=KFPT),DIMENSION(:,:),ALLOCATABLE :: MAVAIL ALLOCATE(int_state%MAVAIL(IMS:IME,JMS:JME)) REAL(kind=KFPT),DIMENSION(:,:),ALLOCATABLE :: XXX ALLOCATE(int_state%XXX(IMS:IME,JMS:JME))

• Adding variable for history/restart: 1) Add it to a file: ~trunk/src/atmos/nmm/module_SOLVER_INTERNAL_STATE.F90

follow existing example i.e. “ACPREC” REAL(kind=KFPT),DIMENSION(:,:),ALLOCATABLE :: ACPREC CALL SET_VAR_PTR(int_state%VARS,NV,'ACPREC' ,int_state%ACPREC ,(/ IMS,JMS /),(/ IME,JME /) ) 2) Add in output namelist: ~trunk/tests/solver_state.txt

follow same example (“ACPREC”) 'ACPREC'

H R

O -

T

'Accumulated precip (m)'

Restarting model

• • While running original run, turn on restart file writing and choose interval in configure_file: minutes_restart: 120 # Frequency of restart output (minutes) write_rst_nemsio: true # True--> Write restart files in NEMSIO format • Running restarted run: mv nmmb_rst_01_nio_0016h_00m_00.00s restart_file_01_nemsio In configure file: restart: true # True--> A restarted run Submit model as usual, it will find restart file, read in data and continue from that point

Writing time series

• copy file ~trunk/tests/ts_locations.nml to run directory • choose variables in solver_state.txt : 'PBLH' H R O -

T

'PBL height (m)' • ts_locations.nml example: &TS_LOCATIONS NPOINTS=2, POINTS_LON=-106.0, -110.0, / POINTS_LAT=54.0, 50.0